12-30873179-T-A

Variant names:

• chr12-30873179-T-A
• rs192287
• ENST00000648700.1:n.247-5493T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648700.1(LINC00941):​n.247-5493T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,004 control chromosomes in the GnomAD database, including 8,844 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8844 hom., cov: 32)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 0 publications found

Genes affected

LINC00941 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984476	XR_001749062.1	n.390-2532A>T		intron_variant	Intron 1 of 3
LOC107984476	XR_001749063.1	n.390-2532A>T		intron_variant	Intron 1 of 3
LOC107984476	XR_007063260.1	n.390-2532A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00941	ENST00000648700.1	n.247-5493T>A		intron_variant	Intron 2 of 2
LINC00941	ENST00000754109.1	n.327-5493T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49431 AN: 151886 Hom.: 8831 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.323

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.325 AC: 49473 AN: 152004 Hom.: 8844 Cov.: 32 AF XY: 0.324 AC XY: 24052 AN XY: 74290

African (AFR) AF: 0.452 AC: 18741 AN: 41420

American (AMR) AF: 0.247 AC: 3773 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2444 AN: 5160

South Asian (SAS) AF: 0.282 AC: 1360 AN: 4818

European-Finnish (FIN) AF: 0.238 AC: 2515 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18379 AN: 67970

Other (OTH) AF: 0.319 AC: 675 AN: 2114

Alfa AF: 0.132 Hom.: 186

Bravo AF: 0.336

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.61
PhyloP100		-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs192287; hg19: chr12-31026113; COSMIC: COSV69470096;